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Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a…
Abstract: Cover song identification (CSI) focuses on finding the same music with different versions in reference anchors given a query track. In this paper, we propose a novel system named CoverHunter that overcomes the shortcomings of…
Accumulation of standardized data collections is opening up novel opportunities for holistic characterization of genome function. The limited scalability of current preprocessing techniques has, however, formed a bottleneck for full…
We present BlendHunter, a proof-of-concept for a deep transfer learning based approach for the automated and robust identification of blended sources in galaxy survey data. We take the VGG-16 network with pre-trained convolutional layers…
We investigate various phenomenological schemes for the rapid generation of 3D mock galaxy catalogues with a given power spectrum and bispectrum. We apply the fast bispectrum estimator \MODALLSS{} to these mock galaxy catalogues and compare…
Hyperparameter tuning is a fundamental aspect of machine learning research. Setting up the infrastructure for systematic optimization of hyperparameters can take a significant amount of time. Here, we present PyHopper, a black-box…
Automated detection and classification of marine mammals vocalizations is critical for conservation and management efforts but is hindered by limited annotated datasets and the acoustic complexity of real-world marine environments. Data…
Deep autoencoders are often extended with a supervised or adversarial loss to learn latent representations with desirable properties, such as greater predictivity of labels and outcomes or fairness with respects to a sensitive variable.…
Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual…
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated trajectory data using either UNIX or MPI file IO, and it…
Future computing systems, from handhelds to supercomputers, will undoubtedly be more parallel and heterogeneous than todays systems to provide more performance and energy efficiency. Thus, GPUs are increasingly being used to accelerate…
Methods based on hypothesis tests (HTs) in the Haar domain are widely used to denoise Poisson count data. Facing large datasets or real-time applications, Haar-based denoisers have to use the decimated transform to meet limited-memory or…
Accurate genome sequencing can improve our understanding of biology and the genetic basis of disease. The standard approach for generating DNA sequences from PacBio instruments relies on HMM-based models. Here, we introduce Distilled…
The lack of labeled second language (L2) speech data is a major challenge in designing mispronunciation detection models. We introduce SpeechBlender - a fine-grained data augmentation pipeline for generating mispronunciation errors to…
A 100um thick silicon detector with 1mm2 pad readout optimized for sub-nanosecond time resolution has been developed and tested. Coupled to a purposely developed amplifier based on SiGe HBT technology, this detector was characterized at the…
For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
Supervised deep learning has shown state-of-the-art performance for medical image segmentation across different applications, including histopathology and cancer research; however, the manual annotation of such data is extremely laborious.…
This paper presents an underlying framework for both automating and accelerating malware classification, more specifically, mapping malicious executables to known Advanced Persistent Threat (APT) groups. The main feature of this analysis is…
In recent years, a standard computational pathology workflow has emerged where whole slide images are cropped into tiles, these tiles are processed using a foundation model, and task-specific models are built using the resulting…